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all_genes_prelim

Bundled with CTexploreR · provided in inst/extdata, read by path with system.file()

Class
tibble
tbl_df/tbl/data.frame
Dimensions
24,488 × 36
Missing
118,395
Format
rda · xz
version 3 · 1.6 MB
File
inst/extdata/all_genes_prelim.rda
Fingerprint
04d3fd34
About this object
A table with named columnsA bordered table: a header band ruled off from the body with an empty slot over each column where its name goes, and rows of cells under it that share every edge. Nothing is in any of them.

A tibble: a data.frame that prints compactly, never converts strings to factors, never adds row names, and can hold list columns. R object catalogue

Columns
Column
Type
Distinct
Missing
Summary
ensembl_gene_id
character
24,488
0
15 characters
external_gene_name
character
24,488
0
2 – 18 characters
GTEX_category
character
4
0
5 – 19 characters
q75_TPM_somatic
numeric
20,916
0
0 – 39792.2mean 39.77
Min.
0
1st Qu.
0.1741
Median
4.1496
Mean
39.7669
3rd Qu.
21.1272
Max.
39792.2
Std. dev
662
Skewness
49.27
Kurtosis
2624
Zeros
3,568
Outliers
2,4410 low · 2441 high
max_TPM_somatic
numeric
23,021
0
0 – 267405mean 178.7
Min.
0
1st Qu.
2.1853
Median
19.9603
Mean
178.652
3rd Qu.
62.7296
Max.
267405
Std. dev
2537
Skewness
60.22
Kurtosis
5368
Zeros
1,366
Outliers
2,6640 low · 2664 high
ratio_testis_somatic
numeric
22,659
482
0 – 244888·884 +Inf · 482 NaN
Min.
0
1st Qu.
0.1167
Median
0.4249
Mean
43.1207
3rd Qu.
1.0196
Max.
244888
Std. dev
1670.02
Skewness
136.9
Kurtosis
1.999e+4
Zeros
465
Outliers
3,2860 low · 3286 high
+Inf
884
Infinities
left out of every figure above
NaN
482of the missing
Longest gap
20
TPM_testis
numeric
23,391
0
0 – 35091.1mean 36.81
Min.
0
1st Qu.
1.2262
Median
6.9581
Mean
36.8124
3rd Qu.
24.1141
Max.
35091.1
Std. dev
529.694
Skewness
46.88
Kurtosis
2393
Zeros
947
Outliers
2,4720 low · 2472 high
lowly_expressed_in_GTEX
logical
2
0
2,663 true·21,825 false
multimapping_analysis
character
3
21,825
15 – 19 characters
HPA_scRNAseq_celltype_specific_nTPM
character
15,039
9,281
12 – 272 characters
max_HPA_somatic
numeric
5,362
9,375
0 – 265226mean 657.2
Min.
0
1st Qu.
6.1
Median
76.4
Mean
657.223
3rd Qu.
243.4
Max.
265226
Std. dev
5061.26
Skewness
26.31
Kurtosis
1029
Zeros
3,171
Outliers
1,8010 low · 1801 high
Longest gap
39
Leading
9
max_HPA_germcell
numeric
3,007
9,375
0 – 725894mean 218.5
Min.
0
1st Qu.
0
Median
0
Mean
218.535
3rd Qu.
41.2
Max.
725894
Std. dev
7359.51
Skewness
86.93
Kurtosis
7888
Zeros
9,882
Outliers
2,6480 low · 2648 high
Longest gap
39
Leading
9
not_detected_in_somatic_HPA
logical
2
9,375
3,171 true·11,942 false
Longest missing run
39
Leading
9
HPA_ratio_germ_som
numeric
2,415
9,788
0 – 7.6818·2,758 +Inf · 413 NaN
Min.
0
1st Qu.
0
Median
0
Mean
0.2756
3rd Qu.
0
Max.
7.6818
Std. dev
0.7367
Skewness
3.691
Kurtosis
16.05
Zeros
9,469
+Inf
2,758
Infinities
left out of every figure above
NaN
413of the missing
Longest gap
39
Leading
9
percent_of_positive_CCLE_cell_lines
numeric
999
31
0 – 100mean 50.08
Min.
0
1st Qu.
3.3
Median
45.3
Mean
50.079
3rd Qu.
99.7
Max.
100
Std. dev
43.1013
Skewness
0.0435
Kurtosis
-1.799
Zeros
1,574
percent_of_negative_CCLE_cell_lines
numeric
1,001
31
0 – 100mean 46.07
Min.
0
1st Qu.
0.1
Median
41.2
Mean
46.066
3rd Qu.
93.8
Max.
100
Std. dev
42.5157
Skewness
0.1043
Kurtosis
-1.773
Zeros
5,134
max_TPM_in_CCLE
numeric
15,930
31
0 – 225620mean 387.3
Min.
0
1st Qu.
16.08
Median
76.12
Mean
387.315
3rd Qu.
212.12
Max.
225620
Std. dev
2699.21
Skewness
39.19
Kurtosis
2443
Zeros
4
Outliers
2,7540 low · 2754 high
CCLE_category
character
5
0
5 – 15 characters
percent_pos_tum
numeric
3,408
5
0 – 100mean 57.24
Min.
0
1st Qu.
6.2058
Median
74.6007
Mean
57.238
3rd Qu.
99.9214
Max.
100
Std. dev
43.0369
Skewness
-0.2504
Kurtosis
-1.748
Zeros
309
percent_neg_tum
numeric
3,426
5
0 – 100mean 37.5
Min.
0
1st Qu.
0
Median
11.1286
Mean
37.5025
3rd Qu.
86.9468
Max.
100
Std. dev
41.6698
Skewness
0.464
Kurtosis
-1.572
Zeros
6,535
max_TPM_in_TCGA
numeric
24,287
5
0 – 273960mean 694.5
Min.
0
1st Qu.
26.5698
Median
101.802
Mean
694.516
3rd Qu.
307.489
Max.
273960
Std. dev
5224.14
Skewness
26.91
Kurtosis
1007
Zeros
70
Outliers
2,8840 low · 2884 high
max_q75_in_NT
numeric
21,479
5
0 – 63111.8mean 88.45
Min.
0
1st Qu.
0.604
Median
9.211
Mean
88.4462
3rd Qu.
37.5106
Max.
63111.8
Std. dev
972.783
Skewness
34.16
Kurtosis
1456
Zeros
1,909
Outliers
2,6090 low · 2609 high
TCGA_category
character
5
4
5 – 18 characters
testis_specificity
character
3
0
15 – 19 characters
CT_gene_type
character
3
0
5 – 8 characters
external_transcript_name
character
24,457
0
0 – 22 characters·32 blank
ensembl_transcript_id
character
24,488
0
15 characters
chromosome_name
character
25
0
1 – 2 characters
strand
integer
2
0
-1 – 1mean 0.0111
Min.
-1
1st Qu.
-1
Median
1
Mean
0.0111
3rd Qu.
1
Max.
1
Std. dev
1
Skewness
-0.0222
Kurtosis
-2
transcript_start
integer
24,470
0
3307 – 248906235mean 7.45e+7
Min.
3307
1st Qu.
3.11416e+7
Median
5.89967e+7
Mean
7.45001e+7
3rd Qu.
1.11492e+8
Max.
248906235
Std. dev
5.61973e+7
Skewness
0.8482
Kurtosis
0.075
Outliers
2610 low · 261 high
transcript_end
integer
24,423
0
4262 – 248919146mean 7.456e+7
Min.
4262
1st Qu.
3.12e+7
Median
59065854
Mean
7.45567e+7
3rd Qu.
1.11542e+8
Max.
248919146
Std. dev
5.62035e+7
Skewness
0.8479
Kurtosis
0.0743
Outliers
2620 low · 262 high
transcription_start_site
integer
24,460
0
3307 – 248906235mean 7.453e+7
Min.
3307
1st Qu.
3.11699e+7
Median
5.90376e+7
Mean
7.45274e+7
3rd Qu.
1.11512e+8
Max.
248906235
Std. dev
5.61999e+7
Skewness
0.8481
Kurtosis
0.0747
Outliers
2610 low · 261 high
transcript_length
integer
7,748
0
112 – 205012mean 3234
Min.
112
1st Qu.
1332
Median
2450
Mean
3233.7
3rd Qu.
4251
Max.
205012
Std. dev
3137.23
Skewness
14.14
Kurtosis
758.3
Outliers
1,1580 low · 1158 high
transcript_biotype
character
2
0
6 – 14 characters
IGV_backbone
character
1
24,409
7 characters
family
character
10
24,368
3 – 5 characters
The same data in 1 other package

This data is identical to the data these packages carry, down to the byte.

CTdata

The structure fingerprint found nothing beyond this list.

Version history
VersionReleasedSizeChangeStored asConfidence
3.232026-04-2824,488 × 36Unchangedrda · xz
version 3 · 1.6 MB
exact
3.222025-10-2924,488 × 36Unchangedrda · xz
version 3 · 1.6 MB
exact
3.212025-04-1524,488 × 36Unchangedrda · xz
version 3 · 1.6 MB
exact
3.202024-10-2924,488 × 36–rda · xz
version 3 · 1.6 MB
exact

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